Publisher Correction: Co-opted transposons help perpetuate conserved higher-order chromosomal structures

Choudhary, Mayank; Friedman, Ryan Z.; Wang, Julia T.; Jang, Hyo Sik; Zhuo, Xiaoyu; Wang, Ting

doi:10.1186/s13059-020-1944-4

Cited by 6 publications

(5 citation statements)

References 1 publication

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“…For instance, we identified an intronic STAT1 binding site derived from a primate-specific TE in the human DICER1 locus. While we did not uncover consistent evidence supporting IFNG-inducible regulation of human DICER1 , these observations align with the concept of convergent regulatory evolution, in which similar expression patterns are perpetuated by the co-option of lineage-specific TEs ( Choudhary et al, 2020 ; Sundaram et al, 2014 ). Therefore, as B2_Mm2 elements shaped the evolution of rodent immune regulatory networks, individual co-option events may have mediated either divergence or preservation of gene expression patterns.…”

Section: Discussionsupporting

confidence: 49%

Mouse B2 SINE elements function as IFN-inducible enhancers

Horton

Kelly

Dziulko

et al. 2023

eLife

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Regulatory networks underlying innate immunity continually face selective pressures to adapt to new and evolving pathogens. Transposable elements (TEs) can affect immune gene expression as a source of inducible regulatory elements, but the significance of these elements in facilitating evolutionary diversification of innate immunity remains largely unexplored. Here, we investigated the mouse epigenomic response to type II interferon (IFN) signaling and discovered that elements from a subfamily of B2 SINE (B2_Mm2) contain STAT1 binding sites and function as IFN-inducible enhancers. CRISPR deletion experiments in mouse cells demonstrated that a B2_Mm2 element has been co-opted as an enhancer driving IFN-inducible expression of Dicer1. The rodent-specific B2 SINE family is highly abundant in the mouse genome and elements have been previously characterized to exhibit promoter, insulator, and non-coding RNA activity. Our work establishes a new role for B2 elements as inducible enhancer elements that influence mouse immunity, and exemplifies how lineage-specific TEs can facilitate evolutionary turnover and divergence of innate immune regulatory networks.

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Section: Discussionsupporting

confidence: 49%

Mouse B2 SINE elements function as IFN-inducible enhancers

Horton

Kelly

Dziulko

et al. 2023

eLife

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“…And 63 out of 64 sites for CTCF AID2/dZF10 decreased site cluster 5 could be assigned to LINE L1. It has been reported that LTR13/LTR41/LINE elements were associated with CTCF [ 49 ]. Our study confirmed this observation and further suggested specifical ZFs can be related to the individual transposable element type.…”

Section: Resultsmentioning

confidence: 99%

Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation

et al. 2023

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Background CTCF is a well-established chromatin architectural protein that also plays various roles in transcriptional regulation. While CTCF biology has been extensively studied, how the domains of CTCF function to regulate transcription remains unknown. Additionally, the original auxin-inducible degron 1 (AID1) system has limitations in investigating the function of CTCF. Results We employ an improved auxin-inducible degron technology, AID2, to facilitate the study of acute depletion of CTCF while overcoming the limitations of the previous AID system. As previously observed through the AID1 system and steady-state RNA analysis, the new AID2 system combined with SLAM-seq confirms that CTCF depletion leads to modest nascent and steady-state transcript changes. A CTCF domain sgRNA library screening identifies the zinc finger (ZF) domain as the region within CTCF with the most functional relevance, including ZFs 1 and 10. Removal of ZFs 1 and 10 reveals genomic regions that independently require these ZFs for DNA binding and transcriptional regulation. Notably, loci regulated by either ZF1 or ZF10 exhibit unique CTCF binding motifs specific to each ZF. Conclusions By extensively comparing the AID1 and AID2 systems for CTCF degradation in SEM cells, we confirm that AID2 degradation is superior for achieving miniAID-tagged protein degradation without the limitations of the AID1 system. The model we create that combines AID2 depletion of CTCF with exogenous overexpression of CTCF mutants allows us to demonstrate how peripheral ZFs intricately orchestrate transcriptional regulation in a cellular context for the first time.

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“…In addition to a direct effect on genes, some TFBS generated by TEs can affect the three-dimensional organization of chromatin and thus participate in the regulation of genes that are not in close proximity. This process is exemplified in mammals where many of the CTCF TFBS, which play an important role in the definition of topologically associated domains (TADs), are derived from TEs [182,183]. A similar effect of TEs on the spatial organization of the genome is found in plants where miniature inverted-repeat transposable elements (MITEs) are associated in rice and sorghum with the presence of matrix attachment regions, which serve as anchors for loops [184].…”

Section: The Impact Of Tes On Gene Regulationmentioning

confidence: 95%

“…Either through exaptation or positive selection on new insertions, TEs have been an important source of evolutionary novelties and have been instrumental in the evolution of biological processes that have affected the diversification of eukaryotes [283]. For instance, many of the traits that are responsible for the evolutionary success of mammals have been profoundly impacted by TEs, from placenta formation [182,202] to the evolution of a complex brain [199,284]. TEs could also affect the diversification of life by directly driving the formation of species [285,286].…”

Section: The Role Of Tes In the Diversification Of Lifementioning

confidence: 99%

The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes

Almojil

Bourgeois

Falis

et al. 2021

Genes

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Transposable elements (TEs) are nearly ubiquitous in eukaryotes. The increase in genomic data, as well as progress in genome annotation and molecular biology techniques, have revealed the vast number of ways mobile elements have impacted the evolution of eukaryotes. In addition to being the main cause of difference in haploid genome size, TEs have affected the overall organization of genomes by accumulating preferentially in some genomic regions, by causing structural rearrangements or by modifying the recombination rate. Although the vast majority of insertions is neutral or deleterious, TEs have been an important source of evolutionary novelties and have played a determinant role in the evolution of fundamental biological processes. TEs have been recruited in the regulation of host genes and are implicated in the evolution of regulatory networks. They have also served as a source of protein-coding sequences or even entire genes. The impact of TEs on eukaryotic evolution is only now being fully appreciated and the role they may play in a number of biological processes, such as speciation and adaptation, remains to be deciphered.

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Publisher Correction: Co-opted transposons help perpetuate conserved higher-order chromosomal structures

Abstract: Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Cited by 6 publications

References 1 publication

Mouse B2 SINE elements function as IFN-inducible enhancers

Mouse B2 SINE elements function as IFN-inducible enhancers

Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation

The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes

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